Now, this is normal for an MMO. When a big content patch comes out, it’s also an excuse to update other game features, delete obsolete ones or change things around so they fit better in the new system. Now, just about everything gets this treatment on some level, and the Flashpoints and Operations that make up the end-game content are no exception to this rule.
Now, these changes can’t be too big, otherwise players might get edgy about how the content is being treated; plus it renders all the beta testing for fairness pretty obsolete. The big change that’s happened with 1.3 though is the loot.
It’s not a bad change, fortunately. Now, any boss in level 50 Flashpoints will drop even better loot rewards than before, giving players a better chance at progressing to the Hard Mode difficulty instances. You can’t clear Hard Mode without decent gear, after all!
If you want to check out all of the changes, then check the patch notes right here.